CREST structural variation software .2bit file error

[M Stan]

I am attempting to use the CREST software but when I run CREST.pl I get the following error:

Can't open //hg19.2bit to read: No such file or directory

I have the gfServer running with the same hg19.2bit file. The hg19.2bit file is in the same directory as my bam files.

Does anyone know why the file is not being recognized?

[zee]

I believe you can give this file as an option "-t hg19.2bit". I am having a slightly different problem where I get blat/gfClient complaining about the incorrect options been given to it by CREST.
Have you seen a similar problem? if so what version of BLAT/gfClient are you using?

[jmwang]

When you supply the 2bit file, please make sure to use the full path as CREST will change the working directory to a temporary one. Also before using CREST, test the gfServer with gfClient and make sure it works.

[mamons]

I am attempting to use the CREST software but when I run CREST.pl I get the following error:



I have the gfServer running with the same hg19.2bit file. The hg19.2bit file is in the same directory as my bam files.

Does anyone know why the file is not being recognized?

Hello,

I get the exact same error even if i specify the full path to the .2bit file, anyone else?

[mamons]

Hello,

I get the exact same error even if i specify the full path to the .2bit file, anyone else?

The problem is solved, at least for me!

I had to specify the full path to the 2bit-genome for the t-flag, that is:

-t path/to/genome/hg19.2bit

as stated above, but the trick was to also use the flag

--2bitdir path/to/genome/

So hope this can help someone else.